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1. The scheduled run times don't match the actual run times! For example, Z7 said it was finished 6 minutes after the previous zone (Z6) said it was finished. But z7 was scheduled for 13 minutes. Why?

2. When the ESP-SMT was first programmed, the watering window was set for 4:00-7:30am. That wasn't enough, so I changed it to 2:30-6:30. The new end time was respected (the unit shut off at 6:30, it said), but the new start time was not respected, it seems. The first "DONE" time, Zone 6, was at 5:06am. Given that zone 6 was scheduled for 64 minutes, perhaps it actually started at 4am (since the actual run times seem to be a bit shorter than the scheduled times). But why didn't the unit start at the 2:30 start-of-window time?

The brain of this smart controller is either well beyond mere mortals, or it is behaving very strangely!

If I were in your spot I'd completely wipe/reset the controller, start completely from scratch.
Allow plenty of time.

I see two ways to "reset" the controller. There's "restore to factory settings" via the front panel, and there is a (magic?) "reset" button on the rear of the front panel (see diagram on p. 57 of the manual).

Any idea which option to choose? (I suppose I can always try and see what it does!)

Optimal window is 24 hrs/7 days a week. Depending on the layout of your yard and zone criteria you programmed, you're not leaving much room for the controller to do what you want it to do. 9 zones in 4 hrs doesn't leave much room for cycle/soak. I could barely water a 9 zone system on a conventional controller in that amt. of time. I don't know if you have certain days of the week off, also. I would at least set the kick in time to sun down, and the kick out time at 7-8a.m.